Karp Cell and Molecular Bio Chpt 5

metabolism

the collection of biochemical reactions that occur within a cell

metabolic pathways

sequences of chemical reactions, each catalyzed by a specific enzyme. Usually confined to specific locations. Convert substrates into end products via a series of metabolic intermediates

catabolic pathways

pathways that break down complex substrates into simpler end products to 1) provide raw materials for the cell and 2) provide chemical energy for the cell

anabolic pathways

pathways that synthesize complex end products from simpler substrates. They 1) require energy and 2) use the ATP and NADPH from catabolic pathways

redox reaction

A chemical reaction involving the transfer of one or more electrons from one reactant to another; also called oxidation-reduction reaction.

reducing agent

the substrate that donates electrons in a redox reactions

oxidizing agent

the substrate that gains electrons in a redox reaction

glycolysis

the first stage in the oxidation of glucose, and occurs in the soluble part of the cytoplasm. Produces pyruvate, NADH, and two molecules of ATP.

tricarboxylic cycle (TCA)

the second stage of the oxidation of glucose, occurs in the mitochondria of eukaryotic cells

dehydrogenase

enzymes that oxidize and reduce cofactors in glycolysis

oxidative phosphorylation

Part of the electron transport chain. A process occurring in the mitochondria that results in the formation of ATP from the flow of electrons across the inner membrane to bind with oxygen.

substrate-level phosphorylation

occurs when ATP is formed by a kinase enzyme. The formation of ATP by an enzyme directly transferring a phosphate group to ADP from an intermediate substrate in catabolism; occurs during glycolysis and the TCA cycle. Succinyl CoA hydrolysis drives the formation of an energy-rich phosphate bond. In animals, it forms GTP, which is used to synthesize ATP by the actions of nucleoside diphosphate.

transfer potential

A measure of the ability of a molecule to transfer any group to another molecule, with molecules having a higher affinity for the group being the better acceptors and molecules having a lower affinity better donors.

anaerobic pathway

pathway that occurs in the absence of oxygen

fermentation

restores NAD+ from NADH. Under anaerobic conditions, glycolysis depletes the supply of NAD+ by reducing it to NADH. This process oxidizes NADH to NAD+ by reducing pyruvate to either lactate or ethanol.

Reducing power

represented by the supply of NADPH in cell

transhydrogenase

catalyzes the transfer of hydrogen atoms from one cofactor to another. NADPH is favored when energy is abundant, NADH is used to make ATP when energy is scarce

protein kinases

Regulate covalent modification of enzymes by phosphorylation, transfers phosphate groups from ATP to a protein, common way for controlling protein activity, used as metabolic regulation

allosteric modulation

when a protein contains two binding sites, the noncovalent binding of a ligand to one site can alter the shape of the second binding site and, therefore, the binding characteristics of that site. Form of metabolic regulation

feedback inhibition

the product of the pathway allosterically inhibits one of the first enzymes of the pathway

gluconeogenesis

anabolic pathway of glucose metabolism. (reverse of glycolysis). Do not proceed via the same reactions as the catabolic pathways even though they may have steps in common. the irreversible steps in catabolic pathways are catalyzed by different enzymes than those in anabolic pathways

anaerobes

organisms that capture and utilize energy by oxygen-independent metabolism

aerobes

organisms that use oxygen to extract more energy from organic molecules

mitochondrion

the site of aerobic respiration in eukaryotes

mitochondrial matrix

The compartment of the mitochondrion enclosed by the inner membrane and containing enzymes and substrates for the TCA cycle.

intermembrane space

the region between the inner membrane and the outer membrane of a mitochondrion or a chloroplast. its main function is nucleotide phosphorylation.

cristae

where the machinery for ATP is located, folded sheets of inner membrane in the mitochondria

inner membrane boundry

one domain of the inner mitochondrial membrane, not the cristae

porin

pore-forming protein found in the outer mitochondrial membrane, often a b-sheet barrel that forms an opening for passage of moderate sized molecules

decarboxylation

A reaction in which a molecule of CO2 is removed from a carboxyl group of an organic acid.

acetyl CoA

formed when pyruvate actively transported across the inner mitochondrial membrane and is decarboxylated. Links glycolysis and TCA cycle

pyruvate dehydrogenase

huge protein complex that catalyzes the decarboxylation of pyruvate, formation of acetyl CoA and production of NADH and H+, and CO2. A group of three enzymes that decarboxylates pyruvate, creating an acetyl group and carbon dioxide. The acetyl group is then attached to coenzyme A to produce acetyl-CoA, a substrate in the Krebs cycle. In the process, NAD+ is reduced to NADH.

oxaloacetate

in the first step of the TCA cycle, it is condensed with two-carbon acetyl group to form the six carbon citrate. It is regenerated by the end of the TCA cycle

citrate

formed in the first step of the TCA cycle when two-carbon acetyl group is condensed with the four carbon oxaloacetate

chemiosmosis

coupling of H+ translocation to ATP synthesis

glycerol-3-phosphate shuttle

Electron carrier that reduces FAD

malate-aspartate shuttle

electron carrier that reduces NAD+

Redox potentials

strong oxidizing agents have a high affinity for electrons, strong reducing agents have a weak affinity for electrons. Redox rxns are accompanied by a decrease in free energy (this energy release is coupled to conformational changes in electron carriers, the changes then move protons across the inner membrane into the intermembrane space). Electrons are passed along the electron transport chain from one acceptor to another.

electron transport chain

Made up of specific electron carriers where electrons are associated with either NADH or FADH2 to move electrons through the inner membrane via a series of carriers of decreasing redox potential

Flavoproteins

type of electron carrier. Polypeptide with either FAD (complex 1) or FMN (complex 2) prosthetic groups (coenzymes) that is capable of donating or accepting 2 protons and 2 electrons.

cytochromes

type of electron carrier that contains heme prosthetic groups with iron. Alternates between Fe2+ and Fe 3+ by gain or loss of a single electron (a,a1,b,c,c1)

Three copper atoms

type of electron carrier that is located with a single protein complex. These accept or donate a single electron as they alternate between Cu2+ and Cu3+

Iron Sulfur proteins

type of electron carrier that contain iron linked to non-heme sulfur centers. Capable of accepting or donating a single electron, over a dozen are identified in mitochondria

Ubiquinone (coenzyme Q)

type of electron carrier that doesn't have a prosthetic group. It is lipid soluble (contains a long hydrophobic chain) and is capable of rapid lateral diffusion. Can accept and donate 2 electrons and protons.

proton-motive force

the storing of energy as a combination of a proton and voltage gradient across a membrane

Complex I

NADH dehydrogenase. Catalyzes transfer electron pair from NADH to ubiquinone. Involves the translocation of 4 protons with passage of each pair of electrons through complex

Complex II

Succinate dehydrogenase. Contains FAD, catalyzes the reaction in the TCA cycle generating FADH2. Transfers electrons to ubiquinone (not accompanied by a proton transfer)

Ubiquinone

Mobile electron carrier. Pool of molecules in inner lipid bilayer, diffuses through membrane from complex I and complex II to complex III. Picks up one proton for each electron it carries

Complex III

Cytochrome bc1. Accepts electrons from ubiquinol and passes them to cytochrome c. 4 protons transferred with passage of electron pair through complex (2 protons from ubiquinol and 2 protons from the matrix)

cytochrome c

peripheral protein associated with the surface facing the intermembrane space. Mobile carrier between Complex III and IV

Complex IV

cytochrome oxidase. A large complex that adds four electrons to O2 to form two molecules of H20. Energy released by O2 reduction is thought to drive conformational changes. These changes promote H+ ions movement through the protein

tunneling pathways

pathways consisting of a series of covalent and hydrogen bonds that stretch across parts of several amino acid residues through which electrons flow

pH gradient

the proton concentration gradient between matrix and intermembrane space creates this gradient

ATP synthase

complex that synthesizes and hydrolyzes ATP. The F1 particle is the catalytic portion, and contains 5 distinct subunits. 3 catalytic sites are associated with 3 beta subunits. The F0 particle attaches to the F1 and is embedded in the inner membrane. The F0 base contains a channel through which protons are conducted from the inner membrane space to the matrix

binding change mechanism

movement of protons through ATP synthase alters the binding affinity of the active site. Each active site goes through distinct conformations that have different affinities for substrates and product. ATP is synthesized through rotational catalysis where the stalk of ATP synthase rotates relative to the head

Peroxisomes

membrane bound vesicles that contain oxidative enzymes. Oxidize very-long-chain fatty acids and synthesize plasmalogens. H2O2 is formed in peroxisomes and is broken down by the enzyme catalase